- Artifact roots are not marked as "generated sources".

- To properly mark artifact sources as up-to-date, compilation-start timestamp is advanced for every chunk/group of chunks before starting compilation

java/compiler/impl/testSrc/com/intellij/compiler/BaseCompilerTestCase.java

@@ -35,6 +35,7 @@ import junit.framework.Assert;
 import org.jetbrains.annotations.Nullable;
 import org.jetbrains.jps.util.JpsPathUtil;
 
+import javax.swing.*;
 import java.io.File;
 import java.io.IOException;
 import java.util.Arrays;
@@ -209,10 +210,10 @@ public abstract class BaseCompilerTestCase extends ModuleTestCase {
   private CompilationLog compile(final ParameterizedRunnable<CompileStatusNotification> action) {
     final Ref<CompilationLog> result = Ref.create(null);
     final Semaphore semaphore = new Semaphore();
+    semaphore.down();
     UIUtil.invokeAndWaitIfNeeded(new Runnable() {
       @Override
       public void run() {
-        semaphore.down();
 
         CompilerManagerImpl.testSetup();
         final CompileStatusNotification callback = new CompileStatusNotification() {
@@ -240,14 +241,18 @@ public abstract class BaseCompilerTestCase extends ModuleTestCase {
       }
     });
 
-    long start = System.currentTimeMillis();
+    final long start = System.currentTimeMillis();
     while (!semaphore.waitFor(10)) {
       if (System.currentTimeMillis() - start > 60 * 1000) {
         throw new RuntimeException("timeout");
       }
+      if (SwingUtilities.isEventDispatchThread()) {
+        UIUtil.dispatchAllInvocationEvents();
+      }
+    }
+    if (SwingUtilities.isEventDispatchThread()) {
       UIUtil.dispatchAllInvocationEvents();
     }
-    UIUtil.dispatchAllInvocationEvents();
 
     return result.get();
   }

jps/jps-builders/src/org/jetbrains/jps/incremental/CompileContext.java

@@ -49,6 +49,8 @@ public interface CompileContext extends UserDataHolder, MessageHandler {
 
   long getCompilationStartStamp();
 
+  void updateCompilationStartStamp();
+
   void markNonIncremental(ModuleBuildTarget target);
 
   void clearNonIncrementalMark(ModuleBuildTarget target);

jps/jps-builders/src/org/jetbrains/jps/incremental/CompileContextImpl.java

@@ -5,7 +5,8 @@ import com.intellij.openapi.util.UserDataHolderBase;
 import com.intellij.util.EventDispatcher;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
-import org.jetbrains.jps.*;
+import org.jetbrains.jps.ModuleChunk;
+import org.jetbrains.jps.ProjectPaths;
 import org.jetbrains.jps.api.CanceledStatus;
 import org.jetbrains.jps.builders.java.JavaModuleBuildTargetType;
 import org.jetbrains.jps.builders.logging.BuildLoggingManager;
@@ -34,7 +35,7 @@ public class CompileContextImpl extends UserDataHolderBase implements CompileCon
   private final Set<ModuleBuildTarget> myNonIncrementalModules = new HashSet<ModuleBuildTarget>();
 
   private final ProjectPaths myProjectPaths;
-  private final long myCompilationStartStamp;
+  private volatile long myCompilationStartStamp;
   private final ProjectDescriptor myProjectDescriptor;
   private final Map<String, String> myBuilderParams;
   private final CanceledStatus myCancelStatus;
@@ -64,6 +65,11 @@ public class CompileContextImpl extends UserDataHolderBase implements CompileCon
     return myCompilationStartStamp;
   }
 
+  @Override
+  public void updateCompilationStartStamp() {
+    myCompilationStartStamp = System.currentTimeMillis();
+  }
+
   @Override
   public ProjectPaths getProjectPaths() {
     return myProjectPaths;

jps/jps-builders/src/org/jetbrains/jps/incremental/IncProjectBuilder.java

@@ -466,6 +466,7 @@ public class IncProjectBuilder {
             }
           }
           finally {
+            context.updateCompilationStartStamp();
             pd.dataManager.closeSourceToOutputStorages(groupChunks);
             pd.dataManager.flush(true);
           }
@@ -478,6 +479,7 @@ public class IncProjectBuilder {
             buildChunkIfAffected(context, scope, chunk);
           }
           finally {
+            context.updateCompilationStartStamp();
             pd.dataManager.closeSourceToOutputStorages(Collections.singleton(chunk));
             pd.dataManager.flush(true);
           }

jps/jps-builders/src/org/jetbrains/jps/incremental/artifacts/instructions/ArtifactRootDescriptor.java

@@ -94,6 +94,6 @@ public abstract class ArtifactRootDescriptor extends BuildRootDescriptor {
 
   @Override
   public boolean isGenerated() {
-    return true;//todo[nik] we cannot detect if this root is generated by some other compiler (e.g. javac) so threat all roots as generated for now
+    return false;//todo[nik] we cannot detect if this root is generated by some other compiler (e.g. javac) so treat all roots as non-generated for now
   }
 }